Tanto las bases de datos de la cantidad de especies y las ASP fueron birndados por el profesor.Ademas se cargo una capa raster con la base de datos “WorldClim” para visualizar la altitud del pais.
library(sf)
## Linking to GEOS 3.9.0, GDAL 3.2.1, PROJ 7.2.1
library(raster)
## Loading required package: sp
library(dplyr)
##
## Attaching package: 'dplyr'
## The following objects are masked from 'package:raster':
##
## intersect, select, union
## The following objects are masked from 'package:stats':
##
## filter, lag
## The following objects are masked from 'package:base':
##
## intersect, setdiff, setequal, union
library(spData)
library(leaflet)
library(plotly)
## Loading required package: ggplot2
##
## Attaching package: 'plotly'
## The following object is masked from 'package:ggplot2':
##
## last_plot
## The following object is masked from 'package:raster':
##
## select
## The following object is masked from 'package:stats':
##
## filter
## The following object is masked from 'package:graphics':
##
## layout
library(DT)
library(tidyr)
##
## Attaching package: 'tidyr'
## The following object is masked from 'package:raster':
##
## extract
# Carga de datos
provincias <-
st_read(
"https://raw.githubusercontent.com/gf0604-procesamientodatosgeograficos/2021i-datos/main/ign/delimitacion-territorial-administrativa/cr_provincias_simp_wgs84.geojson",
)
## Reading layer `cr_provincias_simp_wgs84' from data source `https://raw.githubusercontent.com/gf0604-procesamientodatosgeograficos/2021i-datos/main/ign/delimitacion-territorial-administrativa/cr_provincias_simp_wgs84.geojson' using driver `GeoJSON'
## Simple feature collection with 7 features and 7 fields
## Geometry type: MULTIPOLYGON
## Dimension: XY
## Bounding box: xmin: -87.10189 ymin: 5.498569 xmax: -82.55287 ymax: 11.21964
## Geodetic CRS: WGS 84
orq <-
st_read(
"https://raw.githubusercontent.com/gf0604-procesamientodatosgeograficos/2021i-datos/main/gbif/orchidaceae-cr-registros.csv",
options = c(
"X_POSSIBLE_NAMES=decimalLongitude",
"Y_POSSIBLE_NAMES=decimalLatitude"
),
quiet = TRUE
)
asp <-
st_read(
"https://raw.githubusercontent.com/gf0604-procesamientodatosgeograficos/2021i-datos/main/sinac/asp/asp-wgs84.geojson",
quiet = TRUE
)
alt <- getData(
"worldclim",
var = "alt",
res = .5,
lon = -84,
lat = 10
)
altitud <-
alt %>%
crop(provincias) %>%
mask(provincias)
rcol <- colorNumeric(c("#00CC00", "#FFFF66", "#FF0000"),
values(altitud),
na.color = "transparent")
st_crs(asp) = 4326
st_crs(orq) = 4326
## filtros
orq$species[orq$species == ""] <- "No"
orq <- orq %>%
filter(!is.na(coordinateUncertaintyInMeters) & coordinateUncertaintyInMeters <= 1000)%>%
filter(species!="No")
asp <- asp %>%
filter(descripcio!="Area Marina de Manejo"&descripcio!="Area marina protegida")
asp_registros <-
asp %>%
st_join(orq) %>%
group_by(nombre_asp) %>%
summarize(especies = n_distinct(species,na.rm = TRUE))
## although coordinates are longitude/latitude, st_intersects assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
## although coordinates are longitude/latitude, st_union assumes that they are planar
El siguiente mapa muestra la cantidad de especies de orquideas en Costa rica repartidas en diferentes Areas Silvestres Protegidas (ASP) del pais.
## popups
pasp <- paste0("<b>", "Area protegia: ","</b>",
(asp_registros$nombre_asp),"<br>",
"<b>","Area_km: ","</b>",
(asp$area_km),"<br>",
"<b>", "Cantidad de especies: ","</b>",
(asp_registros$especies),"<br>",
"<b>", "Descripcion ASP: ","</b>",
(asp$descripcio))
# Paleta de colores
colores_registros <-
colorNumeric(palette = "RdPu",
domain = asp_registros$especies,
na.color = "transparent")
# Mapa Leaflet
leaflet() %>%
addTiles(group = "OSM") %>%
addRasterImage(
altitud,
colors = rcol,
opacity = 0.8,
group = "Altitud")%>%
addPolygons(
data = asp_registros,
fillColor = ~ colores_registros(asp_registros$especies),
fillOpacity = 0.7,
stroke = TRUE,
color = "black",
weight = 1,
popup = pasp,
group = "ASP - especies de orquideas"
) %>%
addLayersControl(baseGroups = c("OSM"),
overlayGroups = c("ASP - especies de orquideas", "Altitud")) %>%
addLegend(
position = "bottomleft",
pal = colores_registros,
values = asp_registros$especies,
group = "ASP - especies de orquideas",
title = "Cantidad de especies")
## Warning in showSRID(uprojargs, format = "PROJ", multiline = "NO", prefer_proj =
## prefer_proj): Discarded ellps WGS 84 in Proj4 definition: +proj=merc +a=6378137
## +b=6378137 +lat_ts=0 +lon_0=0 +x_0=0 +y_0=0 +k=1 +units=m +nadgrids=@null
## +wktext +no_defs +type=crs
## Warning in showSRID(uprojargs, format = "PROJ", multiline = "NO", prefer_proj =
## prefer_proj): Discarded datum World Geodetic System 1984 in Proj4 definition
## Warning in showSRID(uprojargs, format = "PROJ", multiline = "NO", prefer_proj =
## prefer_proj): Discarded ellps WGS 84 in Proj4 definition: +proj=merc +a=6378137
## +b=6378137 +lat_ts=0 +lon_0=0 +x_0=0 +y_0=0 +k=1 +units=m +nadgrids=@null
## +wktext +no_defs +type=crs
## Warning in showSRID(uprojargs, format = "PROJ", multiline = "NO", prefer_proj =
## prefer_proj): Discarded datum World Geodetic System 1984 in Proj4 definition